Package: IgGeneUsage
Type: Package
Title: Differential gene usage in immune repertoires
Version: 1.23.0
Authors@R: 
    person(given = "Simo",  
           family = "Kitanovski",
           role = c("aut", "cre"),
           email = "simo.kitanovski@uni-due.de")
Description: Detection of biases in the usage of immunoglobulin (Ig) genes 
    is an important task in immune repertoire profiling. IgGeneUsage detects 
    aberrant Ig gene usage between biological conditions using a probabilistic 
    model which is analyzed computationally by Bayes inference. With this
    IgGeneUsage also avoids some common problems related to the current 
    practice of null-hypothesis significance testing.
License: MIT + file LICENSE
Depends: R (>= 4.2.0)
Imports: methods, reshape2 (>= 1.4.3), Rcpp (>= 0.12.0), RcppParallel
        (>= 5.0.1), rstan (>= 2.18.1), rstantools (>= 2.2.0),
        SummarizedExperiment, tidyr
Suggests: BiocStyle, knitr, rmarkdown, testthat (>= 2.1.0), ggplot2,
        ggforce, ggrepel, patchwork
LinkingTo: BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0),
        RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>=
        2.18.0)
SystemRequirements: GNU make
Encoding: UTF-8
LazyData: false
NeedsCompilation: yes
biocViews: DifferentialExpression, Regression, Genetics, Bayesian,
        BiomedicalInformatics, ImmunoOncology, MathematicalBiology
BugReports: https://github.com/snaketron/IgGeneUsage/issues
URL: https://github.com/snaketron/IgGeneUsage
RoxygenNote: 6.1.1
VignetteBuilder: knitr
Biarch: true
git_url: https://git.bioconductor.org/packages/IgGeneUsage
git_branch: devel
git_last_commit: 073bdd3
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.22
Date/Publication: 2025-06-04
Packaged: 2025-06-05 00:11:09 UTC; biocbuild
Author: Simo Kitanovski [aut, cre]
Maintainer: Simo Kitanovski <simo.kitanovski@uni-due.de>
Built: R 4.5.0; x86_64-w64-mingw32; 2025-06-05 13:12:38 UTC; windows
Archs: x64
